I am using the package maSigPro https://www.bioconductor.org/packages/devel/bioc/vignettes/maSigPro/inst/doc/maSigProUsersGuide.pdf to study the gene expression profiles over time I have a series of data with 7 timepoints and 1,2, or 3 replicates for each one.

>NBData

Time
Replicates
Group1
Group2
Group3
Sample1 0   1   1   0   0
Sample2 0   1   1   0   0
Sample3 1   2   1   0   0
Sample4 1   2   1   0   0
Sample5 1   2   1   0   0
Sample6 2   3   0   1   0
Sample7 2   3   0   1   0
Sample8 2   3   0   1   0
Sample9 3   4   0   1   0
Sample10    3   4   0   1   0
Sample11    4   5   0   1   0
Sample12    5   6   0   0   1
Sample13    5   6   0   0   1
Sample14    5   6   0   0   1
Sample15    6   7   0   0   1
Sample16    6   7   0   0   1
Sample17    6   7   0   0   1

Following the vignette for Next Generation-Sequencing series from the manual,

d <- make.design.matrix(NBdesign)
If we can use maSigPro with theta = 10:
library(MASS)
NBp <- p.vector(NBdata, d, counts=TRUE)
NBt <- T.fit(NBp)

I get the following error:

NBt <- T.fit(NBp, nvar.correction = FALSE)
[1] "fitting  gene 100 out of 259"
[1] "fitting  gene 200 out of 259"
Error in if (group != indepen) { : missing value where TRUE/FALSE needed

What does the error mean? is there a problem on my NBdata? or do I need any extra information on the T.fit function? Seems like the function started working fitting few genes and then brought up the error.

Thanks,